xmapcore 1.15.0
Tim Yates
| Snapshot Date: 2013-10-07 17:00:06 -0700 (Mon, 07 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xmapcore | | Last Changed Rev: 75270 / Revision: 81259 | | Last Changed Date: 2013-04-03 15:06:11 -0700 (Wed, 03 Apr 2013) |
| zin2 | Linux (Ubuntu 12.04.2 LTS) / x86_64 | OK | [ OK ] | |
* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/xmapcore.Rcheck’
* using R Under development (unstable) (2013-10-02 r64018)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xmapcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘xmapcore’ version ‘1.15.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xmapcore’ can be installed ... [6s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.get.correct.column’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘xmapcore/R/zzz.R’:
.onLoad calls:
packageStartupMessage(paste(msg, collapse = "\n"))
See section ‘Good practice’ in '?.onAttach'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'xmapcore.all':
‘all.arrays’ ‘all.chromosomes’ ‘all.domains’ ‘all.est_exons’
‘all.est_genes’ ‘all.est_transcripts’ ‘all.exons’ ‘all.genes’
‘all.prediction_transcripts’ ‘all.probes’ ‘all.probesets’
‘all.proteins’ ‘all.symbols’ ‘all.synonyms’ ‘all.transcripts’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
‘Makefile’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘doRUnit.R’ [5s/5s]
[5s/5s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 5 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/xmapcore.Rcheck/00check.log’
for details.